RetrogeneDB ID: retro_sscr_571

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:54632440..54633966(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSSSCG00000008974
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_sscr_571
TCTAGCTGAAACAATAACAAGCTGCCCAGCAACCTGCCACAGTTACAGTATCTGATCAAGCTGGACCAGCCGGCCTACAT
CAAGGAGTTTCTACAGCATATAATCCCTGCAAATCCAATGTGGAGGTTTTCAAGTTACAACCAAATAAACCCAGCAAAGA
ACTGGCAGAGCTGGTGATGTTTATGGCACAGATTGGTCACTGTTATCCAGAACATCAATGTAACTTTCCTCAAGAACTGA
AAGATCTTCTCTCCTACAGCCACACTGCCCTGAATCCAGATCCCCAAATGATATTTTGCAAAGCTTTGATCTTATTGAGA
AATAAGAATCTCATCAATCCATCAAGTTTGCTAGAACTCTTCTTTGAACTTCTGTGTTGCCATGATAAGCTCCTGCAAAA
CACTTTACTACTCATATTGTGACTGATAGCAAAAATACAAATGCAAAACACAACAATAAGGTGAATGTAGTATTACAGAA
TTTCATGTATACCATGTTACGAAACAGCAATGCACCTGCAGCCACGATATCTTTAGATGTGATGATTGAACTCTACAGAA
GAAACATCTGGAATGATGCCAAAACTGTCAATGTGCTCACAACAGCATATTTCTCTGAGGTCAATGGTTGCTGCTTTAAC
ATTTTTCTTGGAAAAGATGAAGAGGAGAAACAGGGCAGTGACTCAGAATCTGAGGATGACACACCAACAGCAAGAGACCT
GCTAGTGCAGTATGCCATAGGGAAGGAAAGCTCCAAAAACAGGACAAAGTTGGAAAAGGCTGTGAAAGTGCTCTAGAAAC
AAAAGAAGAAGTTAAAAAACAGAAGTGTTCAACTTTTCAGCCATTCATTTGATTCCTGATCCCCAAGGTTTTGCAGAAAA
GCTGCTGAAGCAGCTAGAGAGCTCTAAGGAGAGGTTCTAAGTGAAGATGATGCTCTTGAACCTCACCTCCAGATTGGTAG
GAATTCGCAAGCTTTTTCTCTTCAACTTCTACCCTTTTGTGTAGAGGCTTCTGCAGCCCCACCGAAGAGAAGTAACGAAG
ATCCTTCTGTTTGCTTCACAAGCACCTCATCACTTAGTACCCCCAGAGATCATCCAGTCATTGCTCATGACTGTGGCCAA
CAATATCGTTACCGACACGAACTCTGAGGAAGTCATGACAGTAGGAATCAATGCTATGAAAGAGGTGACAGCTGGATGTC
CTCTGGCTATGACTGAAGAACTTCTCCAAGACCTGGCTCAATATAAAACACATACAGATAAGAATGTGATGATGTCTGCT
AGAACTTTGATTCAGCTCTTCCCAACACTGAATCCTCAGATGTTGCAGAAGAAATTCCAGGGTAAGCCTACAGAGGCATC
CTTAGAAACAAGACTGCAAGAATATGGAGAACTAGAGGCTAAAGATTACATTCAAGGAGCAAATATCCTGGGAGTTGAAA
AAGAAGAAAATGCTGAAGAGGATGAAAATGGGTGGGAGAGTACCAGTCTCAGTAATGAAGCTGACTCCAACAGTGAGTGG
GTCGAC

Alignment

ORF - retro_sscr_571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 74.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSRNNNKLPSNLPQLQNLIKRDPPAYIEEFLQQ-YNHYKSNVEIFKLQPNKPSKELAELVMFMAQIGHCY
          SS.NNNKLPSNLPQLQ.LIK.D.PAYI.EFLQ..YN..KSNVE.FKLQPNKPSKELAELVMFMAQIGHCY
Retrocopy SS*NNNKLPSNLPQLQYLIKLDQPAYIKEFLQH<YNPCKSNVEVFKLQPNKPSKELAELVMFMAQIGHCY

Parental  PEHLSNFPQELKDLLSYNHTVLDPDLRMTFCKALILLRNKNLINPSSLLELFFELLRCHDKLLRKTLY-T
          PEH..NFPQELKDLLSY.HT.L.PD..M.FCKALILLRNKNLINPSSLLELFFELL.CHDKLL..TL..T
Retrocopy PEHQCNFPQELKDLLSYSHTALNPDPQMIFCKALILLRNKNLINPSSLLELFFELLCCHDKLLQNTLL<T

Parental  HIVTDIKNINAKHKNNKVNIVLQNFMYTMLRDSNATAAKISLDVMIELYRRNIWNDAKTVNVITTACFSK
          HIVTD.KN.NAKH.NNKVN.VLQNFMYTMLR.SNA.AA.ISLDVMIELYRRNIWNDAKTVNV.TTA.FS.
Retrocopy HIVTDSKNTNAKH-NNKVNVVLQNFMYTMLRNSNAPAATISLDVMIELYRRNIWNDAKTVNVLTTAYFSE

Parental  VTKILVAALTFFLGKDEEEKQGSDSESEDDTPTARDLLVQYATGKKSSKNKKKLEKAMKVLKKQKKKK-K
          V..........FLGKDEEEKQGSDSESEDDTPTARDLLVQYA.GK.SSKN..KLEKA.KVL.KQKKK..K
Retrocopy VNG---CCFNIFLGKDEEEKQGSDSESEDDTPTARDLLVQYAIGKESSKNRTKLEKAVKVL*KQKKKL>K

Parental  PEVFNFSAIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFVQRFLQPHQR
          .EVFNFSAIHLI.DPQ.FAEKLLKQLESSKERF.VKMML.NL.SRLVGI..LFLFNFYPFV.R.LQPH.R
Retrocopy TEVFNFSAIHLIPDPQGFAEKLLKQLESSKERF*VKMMLLNLTSRLVGIRKLFLFNFYPFV*RLLQPHRR

Parental  EVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLA
          EVTKILLFA.QA.HHLVPPEIIQSLLMTVANN.VTD.NS.EVMTVGINA.KE.TA.CPLAMTEELLQDLA
Retrocopy EVTKILLFASQAPHHLVPPEIIQSLLMTVANNIVTDTNSEEVMTVGINAMKEVTAGCPLAMTEELLQDLA

Parental  QYKTHKDKNVMMSARTLIQLFRTLNPQMLQKKFRGKPTEASLEARVQEYGELDAKDYIPGAEILEVEKEE
          QYKTH.DKNVMMSARTLIQLF.TLNPQMLQKKF.GKPTEASLE.R.QEYGEL.AKDYI.GA.IL.VEKEE
Retrocopy QYKTHTDKNVMMSARTLIQLFPTLNPQMLQKKFQGKPTEASLETRLQEYGELEAKDYIQGANILGVEKEE

Parental  NAEEDGDGWESTSLSDEADSDGEWVD
          NAEED..GWESTSLS.EADS..EWVD
Retrocopy NAEEDENGWESTSLSNEADSNSEWVD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	7.57 RPM
SRP014902_testis	0.00 RPM	26.31 RPM
SRP018288_heart	0.00 RPM	37.30 RPM
SRP018288_kidney	0.59 RPM	41.37 RPM
SRP018288_liver	0.00 RPM	32.46 RPM
SRP018288_lung	0.10 RPM	33.09 RPM
SRP018856_adipose	0.15 RPM	18.86 RPM
SRP035408_brain	0.13 RPM	43.58 RPM
SRP035408_liver	0.00 RPM	45.44 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_571 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_571 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571 ,